An In-Depth Look at Selection Indices: Part 3

We’ve reached the finale in the series of articles discussing the lineup of available selection indices for Shorthorn breeders and customers. After covering the basics of what goes into a selection index in January, and further explaining $Calving Ease and $Feedlot in February, March finds us with two final pieces of the index puzzle to piece together: $British Maternal Index ($BMI) and $Fescue.

$British Maternal Index

The written definition of $BMI on the ASA website is as follows:

“This multi-trait selection index attempts to measure a bull’s potential profitability when complimenting the British cow base (Angus, Red Angus, Hereford, etc.) in a maternal breeding program. Shorthorn females can likewise be gauged at adding value to British or British-composite bulls of other breeds. A balance of growth (WW) and carcass traits (REA, Fat, MB) are desired with a strong maternal component (CED, Milk, CEM) aimed at moderate mature size (YW), optimum reproductive efficiency and cow longevity.”

A few points of emphasis can be gleaned from this Websteresque definition. First and foremost, you can figure out that there are several traits of interest included in $BMI. In a more comprehensive scenario like this one, there are more traits that become involved. I think you will notice that the production situation outlined in this index is more complex than $Feedlot, and certainly more involved than $Calving Ease. Many of America’s commercial cattle producers have their programs set up with management similar to what is described in $BMI: British-based cows, selling calves at weaning, and retaining replacements heifers.

With most commercial cattlemen selling calves at weaning, the economic drivers of this sector of their enterprise are ive calves and pounds of calf at weaning. With that in mind, it makes perfect sense for the CED and WW EPDs to play a significant part of $BMI. Weaning weight has arguably the most significant impact on $BMI of any included traits. When retaining females for the breeding herd, they need to be able to have a live calf, produce milk to raise that calf, and do so in a moderate mature size. While we have EPDs to measure two of these 3 traits (CEM and Milk), we have to use YW as an indicator trait for mature size since there is a not current EPD for mature cow weight in the Shorthorn genetic evaluation. A higher YW EPD has a more negative impact on $BMI, as bigger YW indicates a larger mature cow size. Even though it is not a direct point of emphasis in the scenario outlined for $BMI, carcass traits (REA, Fat, Marb) do play a role in the calculation, albeit smaller than the other traits outlined. Once these cattle are sold at weaning and enter the feedlot, the ones with the genetic capability to perform on the rail become more valuable to feeders.

When the $BMI index was developed, The American Shorthorn Association did not have a Stayability EPD to include in $BMI. Obviously, the ability of a female to stay in the cow herd productively has an impact on her ability to add profit to the ranch’s bottom line. Like I mentioned in the previous article for $Feedlot, it’s not as easy to edit an index as to just stick the Stayability EPD into the $BMI formula and it still work properly. There have been several discussions amongst staff, ASA BOD and breeders involved in ASA committees on the best way to improve this index going forward.

$Fescue

The youngest and most unique member of the Shorthorn index lineup is $Fescue. The components of $Fescue are very similar to $BMI, but with an added genomic piece to the puzzle. The addition of $Fescue is only for those animals who have had the Fescue Tolerance T-Snip test that is offered by AgBotanica performed and recorded with ASA. The test results are reported on a 0-50 scale, with cattle scoring a 50 considered to be most tolerant of toxic fescue. Research from AgBotanica indicates that cows with incrementally higher scores for the fescue tolerance test weaned off heavier calves than those with lower scores (40s weaned off heavier calves than 30s, who weaned off heavier than 20s, etc.)

The methodology behind $Fescue includes the calculation of $BMI with the Fescue Tolerance test score incorporated into the equation as a weighted factor. With the research conducted by AgBotanica showing how much of an effect the score has on weaning weight produced, it was possible to weight the score into a selection index. The most logical piece to incorporate with $Fescue is $BMI, as a production scenario that is most likely to be impacted by grazing toxic fescue is a cow/calf situation like the one outlined for $BMI.

Wrap Up
With this look into the components of each selection index that is offered to ASA members, hopefully you now have a better idea of what makes up these tools and have more confidence to use them in your mating decisions. As always, these are just a few of the available tools out there to help you breed better cattle. A tool is only useful if it’s used properly, and only using one tool to try and do a complex job (like breeding cattle) can prove very difficult. Use your knowledge of your herd, in addition to the available tools like EPDs and selection indices, to make the most informed decision.

Written by Matt Woolfolk, Director of Performance Programs

An In-Depth Look at Selection Indices: Part 2

I kicked off 2019 by beginning this series on the selection index lineup we have available to Shorthorn breeders and their customers. In the January issue, a basic overview of selection index technology was provided in Part 1. With the concepts of how selection indices are constructed laid out, it’s time to go deeper into the specific indices that are available in the Shorthorn genetic evaluation. In this installment, I’m going to provide you some more information on two of our selection indices; $Calving Ease and $Feedlot.

$Calving Ease ($CEZ)
The $Calving Ease index in our genetic evaluation is the simplest in terms of the number of traits included. This index is designed to identify the bulls that are best suited for use in breeding heifers. Bulls with a high $CEZ value are the bulls that are expected to sire offspring that calve unassisted and then grow out to a moderate mature weight. To meet that goal, the EPDs included in $CEZ are Calving Ease Direct (CED) and Yearling Weight (YW). CED is weighted heavily in this index, while YW is taken into consideration as an indicator trait for mature weight, which we do not have an EPD for currently. Higher growth cattle (the ones with really high YW EPDs) will see their $CEZ impacted more heavily than moderate YW EPD cattle, as the index is designed to select for cattle that will reach a moderate mature weight. Currently, the average of all non-parent cattle in the Shorthorn database for $CEZ is 28.10. Cattle in the top 25% of the breed have a $CEZ of 36.56 or greater, while cattle in the top 10% will boast a 46.10 or greater $CEZ.

$Feedlot ($F)
For those of you who retain ownership of feeder cattle, or might have customers that do so, the $Feedlot index is designed with that production scenario in mind. Sires that excel in $F are expected to sire feeder calves that will grow rapidly and produce a carcass that can grade very well on a quality scale. The $Feedlot has a few more pieces to it when compared to $Calving Ease. The EPDs included in $F include CED, Weaning Weight (WW), YW, Fat, Ribeye Area (REA), and Marbling (MB).

I’m sure the first thing that catches your attention from this list is the inclusion of CED. CED is incorporated into $F because even though this is a terminal index with growth and end product emphasized, completely ignoring calving ease could lead to dystocia problems, even in a terminally-focused operation. Therefore, CED is included in $F, albeit in a smaller emphasis than the other traits involved. As you would expect, growth and carcass merit are highlighted in $F. Of all of the carcass traits (Fat, REA, and MB), MB is more heavily emphasized than the others, as quality-based premiums and improving carcass quality grade are increasingly important in the industry. Both growth traits are more heavily emphasized in $F than CED and the carcass traits. After all, even at harvest, cattle are still sold by the pound, and cattle that grow are more likely to produce heavier (and more valuable) carcasses. Yearling Weight is used as an indicator trait for Carcass Weight, with the reasoning being that when $F was developed several years ago, there was no Carcass Weight EPD to include. Unfortunately, implementing Carcass Weight in place of YW is not as simple as taking one number out and putting another in.

As of the time that this was written, the average of non-parent Shorthorn cattle for $F is 52.35. For an animal to be in the Top 25%, the $F must be 54.51 or greater, and a $F of 57.04 qualifies in the Top 10% of non-parent Shorthorns. Hopefully, having some insight into what goes into our stable of selection indices gives you a better idea of how they might be beneficial to use in your breeding programs. It’s hard to use something when you don’t understand how it works, whether it is a power tool, an electronic device, or a selection index. In the next issue of Shorthorn Country, Part 3 of this series will tackle the $British Maternal Index, as well as the $Fescue.

Written by Matt Woolfolk, ASA Director of Performance Programs

An In-Depth Look at Selection Indices: Part 1

A hot topic in the hallway at the ASA Annual Meeting in Kansas City was the use of selection indices and the tools we have available in the Shorthorn breed. Selection index technology wasn’t an official topic in the educational forum, but I believe there was a lot of interest and educating going on among many breeders in attendance. There was a lot of good information and philosophy spread amongst breeders, and I hate that everyone couldn’t be in attendance to be a part of these discussions. That spurred the idea to spend a few months writing about selection indices, how they work, and what we have available in the Shorthorn breed at this time for you to use in your breeding programs. In order to get the best view we can at the whole picture, I think it’s only fitting that we start with the basics before diving into the more specific material.

The development of selection indices in the beef cattle industry are a relatively new addition to genetic evaluations. After EPDs came along, the idea to combine some of those genetic predictors into a single figure to attempt to gauge economic and genetic merit led to the implementation of the selection index. A selection index is intended to give a cattleman a relative economic value for an individual animal when in a specific production scenario. Traits that are important to a scenario are identified and included in an equation. The traits in the equation are weighted based on their economic value in the individual production scenario. Depending on the situation, some traits will be weighted significantly in the calculations, while others may only play a small role in the final output. Simply put, a selection index is like a long, complicated algebra formula, but instead of just X and Y for variables, there are a LOT more, with some indices having nearly enough components to have variables A through Z!

Usually, an association will offer several selection index options to their membership to try and meet several of their breeding objectives. Each index is calculated from a specific production situation, and it is important to know and understand those situations when studying an index. An index built for a breeding program of mature cows may not be as effective for you if you are looking to breed heifers. An index built with retained ownership of feeder cattle in mind may not quite fit your needs (or the needs of your customers) if selling calves at weaning is your main objective. Of course, whatever index is available to you may not be a perfect fit for your operation, but there’s a good chance that one or more indices will fit the needs of your program pretty well.

A selection index is designed to help breeders improve genetic merit without the drawbacks of single trait selection that can sometimes occur when using a single EPD to make breeding decisions. We all know that multiple traits must be taken into consideration when evaluating what makes profitable cattle in any situation, and a selection index is the best tool we have of predicting which animals can work in an environment.

The American Shorthorn Association has four available selection indices available for breeder use in their mating and selection decisions. They include $Calving Ease, $British Maternal Index, $Feedlot and $Fescue. In future issues, I will go into more detail about the components and uses of each index. Identifying traits of importance, the production scenarios designed for each index, and how we can use them as Shorthorn breeders and commercial seedstock producers will be discussed.

In the ever changing world of beef cattle genetic evaluation and selection, the use of the selection index is growing increasingly popular with commercial bull buyers. As providers of commercial seedstock, I hope that you feel it is part of your responsibility to understand and assist your customers in finding and using the proper selection index that meets their operation’s criteria. Hopefully, I will be able to fulfill my responsibility to give you the information you need to accomplish this goal over the next few articles!

Contemporary Grouping: Why, When, and How

Proper contemporary groups are just as important to our database and genetic evaluation as proper data collection. Data and contemporary groups build on each other in order to have a strong genetic evaluation. Contemporary groups can be a bit overwhelming, and rightfully so. Knowing which animals belong together in one group or another can take some time to fully grasp. It’s a topic that has been covered many times, but a little refresher course hasn’t ever hurt anyone. Hopefully by sharing some background information and a few helpful hints, your understanding of contemporary grouping will become clearer.

Why We Need Contemporary Groups
As you know, not all weights and measures are created equally because not all cattle are managed in identical environments.

So how do we use data in genetic evaluations when it’s not all collected on an equal playing field? By utilizing proper contemporary groups! Our EPD calculations are driven by comparisons in performance between animals, rather than actual measurements for a trait. Contemporary groups are used to define which animals are to be compared to each other within a herd. By making sure we compare the right animals to each other, we get the best information available to fuel the EPD calculations. Having weights recorded is important, but having the right weights recorded in a contemporary group together is equally necessary.

When to Worry with Contemporary Groups
I commonly get asked when in the production cycle to start paying attention to contemporary groups. The answer is the day your first calf is born, and every time you collect a new piece of data in your herd. Contemporary groups start when birth records are recorded. It is important to ensure that you have your calves grouped correctly at birth, because all subsequent contemporary groups are based off the initial birth groups. The largest contemporary groups will always be for birth records, since cattle can only be removed from the original contemporary group over time. Every time a new data point is collected, the contemporary group should be examined for animals that might have been treated differently and are no longer fairly compared to the rest of the group. Once an animal is no longer on the same playing field (either advantaged or disadvantaged), they need to be regrouped. If you have a calf that gets really sick between birth and weaning, or if you choose some calves to begin prepping for the show barn, those cattle should be removed from the larger contemporary group. When collecting data such as weaning, yearling, or ultrasound, the date of data collection also dictates contemporary groups. All the calves that need to be in the same weaning contemporary group need to have their weaning weights taken on the same day. If there are multiple weighing days, then you will have multiple contemporary groups.

How to Build Your Contemporary Groups
There are some rules you will want to follow when putting your cattle into the proper contemporary groups. The sex of calf is a major factor, always sorting heifers and bulls into their own groups at birth, and then into heifers, steers, and bulls for any data collected from weaning onward. Grouping calves by calving season is also important. Most breeders calve in smaller windows and don’t have to worry too much with season. However, if you don’t have a tight calving season, it is recommended to group your birth contemporaries into 90-day windows to get a fair comparison. Obviously, management and location are a major factor. If you run cows on multiple ranches, then you will have contemporary groups for each ranch. Fortunately, Digital Beef does a pretty good job of covering some of these bases for you. If you need to manually put cattle into different groups, there are functions available to help you do so, such as the “Season” (birth recording) and “Mgmt” (Weaning) options when recording data.As always, we want to help you if you have any questions with your contemporary groups. Not only does having them done correctly benefit you, but also the rest of the breed as we continue to build our database. A stronger database is the foundation for better EPD calculations.

 

2017 ASA/University of Illinois Sire Test Early Results

Early results are in from the 2017 ASA Sire Test with the University of Illinois, and Shorthorn genetics look to be proving their mettle in a real-world commercial setting. Even though they are heavily involved in cow-calf research, the University of Illinois runs their cow herd as close to a no-nonsense commercial operation as you will find in any university system. It’s a great opportunity to work with cattle that are forced to work in tight breeding seasons, have quality udders, and maintain themselves while raising a calf on minimal supplementation. A special thanks to the breeders who participated in the 2017 Sire Test. Without your support, we wouldn’t be able to gather this valuable information that will help move the Shorthorn breed towards our goals of growing commercial acceptance for our cattle. From September 8- October 4, 151 Shorthorn-sired calves were born, with 91% of the calves born in the 17 day window from September 13- September 30. Using UI’s SimAngus cow herd resulted in 123 black-hided calves, 15 black calves with white markings/blue roans, and 13 red hided calves. These calves were raised without creep feed until weaning on February 14, 2018. After some time to precondition the cattle, they will be shipped to the UI Farm near the university campus this month, where they will go on feed. Data collection in this phase of the trial will include gain, feed efficiency, and eventually carcass data. Initial reports indicate that these weights stack up comparably to other calves within the UI herd, showcasing the value of Shorthorns as the British breed crossbreeding solution. Keep in mind that it can be difficult to draw any conclusions comparing groups of extremely small size. Having only 1 or 2 calves may not be a fair representation of a sire’s genetic capabilities. Unfortunately, nature didn’t bless us with perfect distribution of steer and heifer calves across all sires. Weaning weight data listed is adjusted to a 205 day weaning weight. All data has been uploaded to Digital Beef. We are working with UI to plan a field day in August. This will include a chance to see the cattle on feed, as well as educational presentations and fellowship with other Shorthorn breeders. Be sure to look for more information on this event in future issues of the Shorthorn Country. View Full Report Here!

Saturday August 25: National Shorthorn Sire Test Field Day

Mark your calendar for Saturday, August 25. The ASA and the University of Illinois will be hosting the National Shorthorn Sire Text Field Day.
9:30 a.m. – 12:00 p.m. – Join us on the U of I campus for an educational program as we discuss the ASA Sire Test. Speakers include Dr. Dan Shike from University of Illinois, Matt Woolfolk from ASA and more.
12:00 p.m. – 1:00 p.m. – Lunch catered by the U of I Meat Science Club
1:00 p.m. – 2:00 p.m. –  We will head out to the University Farm to view the calves in the feedlot from the 2017 ASA Sire Test
If you would like to join us for this event, please contact Matt Woolfolk to RSVP (matt@shorthorn.org).

What To Expect From Genomic Testing

The new multi-breed genetic evaluation with the American Simmental Association has been a fairly smooth transition from a data and EPD perspective. Coupled with the database move to Digital Beef, there’s been a lot to digest in the last 12 months. Breeders have done a tremendous job of adopting and understanding the new breed averages and variation versus the old system. Likewise, your dedication to seeing that genomics is a tool in the box for all Shorthorn breeders has been incredible. On the other hand, much to our disappointment, the genomics ‘train’ has been an extremely slow ride with a number of stops, delays, and outright frustrations. Rest assured, the train is still on the tracks and headed in the right direction, albeit at a sluggish pace. This article should help prepare you for when the genomics train finally reaches the station. As well, it will offer insight for when utilizing genomics is a good idea versus other genetic selection tools already in your arsenal.

First of all, it is extremely important breeders understand genomic tests are not the ‘golden egg’ to beef production, maybe just the shiniest one of the dozen. Likewise, genomics cannot replace the need for collecting performance and carcass information on your herd. In reality, data submission is more important than ever to ensure that the money you invest in a genomic test is worth the spend. Like every other column on the paper, a genomic score is only as good as the data behind it, or in front of it (chronologically) in this case. Genomic tests are generated by taking information from higher accuracy animals, then using it to help predict the performance of young, low accuracy animals. As a result, genomics can only enhance the traits we already collect. For example, Shorthorn breeders will not be able to pull a hair or blood sample to enhance udder quality or docility until an EPD for those traits exists.

Which animals in my herd do I test? When do I collect and submit the samples?

In developing the tests, we asked for semen and/or DNA samples on older A.I. sires. Moving forward, there will be no reason to dig in the tank and test old genetics. Genomics cannot help the EPDs of high accuracy animals; they were used as the baseline for comparison to get the breed started towards genomic-enhanced EPDs. The true value of genomics is enhancing young animals not yet old enough to generate progeny, particularly daughters in production. Under the current system, a sire is 4-5 years old before performance data from his daughters can affect his EPD profile. A genomic test can fast forward some traits on the paper as if the bull already has 15 daughters in production! Young bulls or heifers that show promise can be tested as young as 1 month of age. If pulling hair, be sure that the root follicles or “root bulbs” come out with the hair strand. A blood sample may be better for extremely young cattle. Results from the genomic test may help breeders make decisions on how to manage or market that individual.

Many breeders collect DNA samples for genomic testing at either weaning or yearling. The cattle are in the chute, making the collection of hair or blood a part of the routine. Decisions can be made at a later date as to which animals actually get submitted; no need to submit DNA on critters headed to the cull pen or feedlot. In contrast, samples need to be submitted well in advance of printed sale catalogs. For example, if your bulls or females sell in March, submit the DNA in the fall so results enter the genetic evaluation and enhance the EPDs that typically come out in January.

 

What could I learn from the genomic information?

The days of stars and 1-10 scores for individual traits are gone. All genomic results are incorporated into the EPDs of the individual. It is important to note that genomics cannot “enhance” every trait on the paper equally. Unfortunately, some traits are largely controlled by the environment the calf endures; others are much more controlled by genetics. For example, the sex of the calf and the color of the hide are 100% controlled by genetics. No matter what we do to that animal from a management standpoint will not change the sex or the color of the calf at birth. On the other hand, a trait like Maternal Calving Ease EPD has a huge environmental component. How we feed, breed, and manage that cow can largely affect her ability to calve. However, genomics can play a significant role in this trait by offering genetic insight to the likelihood that a bull’s daughter will calve on their own. In a nutshell, the harder the trait is to measure, the more important genomics can become at enhancing the EPD.

Genomics also somewhat rely on the heritability of a trait. Heritability is the measure from 0 to 1 used to describe the level of genetic influence on the trait versus environment. Some look at heritability like a percentage of the phenotype that is ‘inherited’ by genetics. The higher the number, the more genetics influence the result. Marbling is a unique trait where genomics has been successful. Heritability for marbling is considered moderately heritable at approximately 0.30-0.35 for most breeds. A few small segments of the genome in some breeds do a very good job of predicting marbling, so the genomic test is successful. Other traits like Scrotal Circumference have very low heritability (0.10-0.15). If a genomic test can find markers that have a large influence on scrotal circumference, then the test has value. However, if scrotal circumference is truly controlled by thousands of gene segments, then the likelihood a genomic test is useful is very low. Breed to breed, genomics may show real promise for a trait in one breed, but be virtually useless in another breed. As a result, breed associations must independently develop and validate their own genomic tests.

Please don’t let the chart below overwhelm you; it can be very useful in understanding the effect genomics can have on an EPD. The Accuracy from 0 to 1 is down the left side. Individual EPDs are across the top. Keep in mind that some columns are not Shorthorn EPDs…yet. Most all pedigree estimate EPDs (the average of the sire and dam’s EPDs) come in under 0.10 Accuracy. Obviously, if the breeder reports calving ease, birth, weaning, and yearling data on the bull, the Accuracy for the bull’s growth traits can go up to roughly 0.35. Let’s use BW as an example. Patrick Article - ChartIf you buy a yearling bull that is a +2.0 on BW EPD and his Accuracy is 0.10, the chart tells us that 68% of the time (1 standard deviation) the bull’s “true” EPD for BW will be between -0.7 and 4.7. And yes, 32% of the time, his true EPD could be even worse…or even better than that.

If the Shorthorn genomic test is run on that bull, his BW EPD may be +2.5 with an Accuracy of .40. Now, refer to the chart. The bull is now plus or minus 1.8, making his EPD likely between +0.7 and +4.3. We gain confidence that the bull is likely not a candidate for heifers. I would encourage you to enter the following link in your browser and read Dr. Scott Greiner’s article that further explains the chart.

https://www.herdbook.org/simmapp/action/pages.PagesAction/eventSubmit_displayPage/T/pageId/15/

Given our relatively small sample size, genomics for the Shorthorn breed will be an ongoing commitment from breeders of all sizes. The more performance data that gets submitted, the better the genomic tests can become. As an example, if we find a “rock star” bull for Marbling EPD based on ultrasound and the genomic test, we still need to follow his progeny to the rail and collect marbling scores or at least scan his sons and daughters to prove the bull even further. Then, we revalidate the genomic test for Marbling EPD and it becomes even more powerful and more significant as a tool for selection. In the end, genomics can be a real asset to breeders with just a few cows, those that rely heavily on embryo transfer, or breeders with large contemporary groups as they try to find ‘the one’ that will give them an edge or move their herd forward at an accelerated pace. The train is comin’.

Written By: American Shorthorn Association contributor, Patrick Wall

Patrick can be reached at patwall@iastate.edu